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Chapter 6: An Introduction to Energy, Enzymes, and Metabolism

Page history last edited by Derek Weber 11 years, 6 months ago


Learning Objectives 

  • Differentiate between kinetic and potential energy.
  • Understand the First and Second Laws of Thermodynamics and describe how they reflect the existence and behavior of energy in the universe.
  • Define enthalpy, entropy, and free energy, and describe how these concepts affect the fate of chemical reactions.
  • Explain the energy requirements of endergonic and exergonic reactions.
  • Describe how oxidation and reduction are interrelated in chemical reactions.
  • Understand the structure of ATP and describe how ATP makes a wide variety of thermodynamically unfavorable cellular processes possible.
  • Describe the importance of activation energy and how it can be altered.
  • Explain the various ways in which enzymes increase the rate of biological reactions.
  • Explain how cofactors, prosthetic groups and other aspects of the chemical environment affect enzyme activity.
  • Define competitive inhibition, noncompetitive inhibition, and activation and explain how each relates to the active and allosteric sites.
  • Explain the relationship between anabolic and catabolic pathways in metabolism and describe the storage and release of energy in the forms of ATP and NADH.
  • Describe the three major ways cells regulate metabolic pathways.
  • Describe the mechanisms used by cells to recycle components of macromolecules and organelles for use in the synthesis of new molecules and structures.
  • Explain how recycling of cellular components reduces the overall energy requirements of the cell. 

 

Chapter Summary

Living organisms transform potential energy into kinetic energy to survive, grow, and reproduce. The energy that the earth receives from the sun is transformed into heat energy as it warms the continents and the oceans. Various kinds of photosynthetic organisms also absorb this energy and convert it to potential energy in the form of chemical bonds.

 

The First Law of Thermodynamics states that energy can be transformed from one state to another, but cannot be created or destroyed. The Second Law of Thermodynamics states that objects tend to move from a state of greater order to one of lesser order. Thus entropy, the measure of disorder in a system, is constantly increasing. The amount of free energy available to form chemical bonds is equal to the energy within a cell that is available to do work (enthalpy) minus the product of temperature and entropy. A reaction proceeds spontaneously when its change in free energy is a negative number.

 

The products of exergonic reactions contain less free energy than the reactants. Such reactions proceed spontaneously and release the excess usable free energy. The products of endergonic reactions have more free energy than the reactants, do not occur spontaneously, and require an input of energy to proceed. Fortunately, even exergonic reactions require an input of a small amount of activation energy to get started. Otherwise all combustible materials would have

burned up long ago. This activation energy is required to destabilize the existing chemical bonds; something that occurs more readily in the presence of a catalyst.

 

The chief energy currency of cells is the molecule adenosine triphosphate, ATP. This molecule is composed of a five-carbon backbone to which a nitrogenous adenine base and a chain of three phosphate groups are attached. The covalent bonds linking the phosphate groups are high ­energy bonds that are readily broken to release 7.3 kcal/mole of energy. All cells use ATP to drive their endergonic reactions. Cells do not store large amounts of ATP but possess a pool of ADP and phosphates so that they can make ATP whenever it is needed.

 

Enzymes are biological catalyzing agents generally in the form of proteins and having names ending in -ase. An enzyme brings two substances together in the proper orientation and stresses certain bonds. It does not force a reaction to occur in a single direction but enhances the reaction in both directions. Although many reactions involve discrete enzymes, many complex pathways depend on multienzyme complexes to efficiently carry out their sequential reactions. Certain RNA reactions possess unique RNA catalysts called ribozymes, giving strength to the argument that RNA evolved prior to proteins. Enzyme activity is altered by several factors including temperature and hydrogen ion concentration (pH). A competitive inhibitor binds at the same site as the substrate, effectively inhibiting the reaction. Non­competitive inhibitors and activators bind to the allosteric site to alter reaction rates. Various cofactors are associated with most enzymes and may be in the form of metal ions or nonprotein, organic molecules called coenzymes. One of the more important coenzymes is nicotinamide adenine dinucleotide (NAD+), a hydrogen acceptor that, when reduced, becomes NADH. This molecule is responsible for carrying the energy of an electron and a hydrogen throughout the cell.

 

Living organisms organize their metabolic activities in reaction chains called biochemical pathways. The first metabolic pathways were anaerobic since oxygen was not present in the early atmosphere of the earth. The product of one reaction becomes the substrate for the next. The step-wise nature of a biochemical pathway reflects its evolution. Organisms rarely evolve new processes completely independent of other processes; rather they utilize the machinery that already exists and add to it or alter it slightly. The addition of new processes generally occurs at the beginning of the pathway; such a pathway evolves backwards. The final reactions evolved first, the beginning reaction is the most recent adaptation. The stepwise progression of pathways allows for more precise regulation.

 

Oxidation-reduction reactions are a class of reactions that pass electrons from one molecule to another. A molecule that is oxidized loses an electron; one that is reduced gains an electron. Oxygen is the most common electron acceptor in biological systems. Since the transfer of electrons is accompanied by a transfer of protons in the form of H+ ions, oxidation generally involves the removal of hydrogen atoms and reduction involves the addition of hydrogen atoms. In biological systems, oxidation-reduction reactions are coupled to one another. In photosynthesis, carbon dioxide is reduced to form glucose, storing energy. In cellular respiration, the oxidation of glucose releases energy.

 

Large molecules in cells do not last forever and cells therefore need to synthesize new macromolecules to replace those that have been used up or that have been degraded. The biosynthetic pathways of cells require raw materials in the form of the respective building blocks of the macromolecules. While cells import amino acids, nucleotides, and sugars for use in anabolic reactions, they also have mechanisms for recycling macromolecules present in the cell. By recycling old, “worn out” cellular components, cells are able to reduce the overall amount of energy required from the environment.

Virtual Lectures 

Section 6.1: Energy and Chemical Reactions

1. Energy

2. ATP

Section 6.2: Enzymes and Ribozymes 

Section 6.3: Overview of Metabolism and Section 6.4: Recycling of Macromolecules

 

** make sure to press OK when the LMS implementation screen appears.

 

Animations

1.  Equilibrium

2.  Enzymes Sustain Life

3.  Energy of Activation

4.  Small Cofactors May Regulate Enzyme Activity: Catalase

5.  Physcial Factors that Regulate Enzyme Activity: Temperature

6.  Feedback Inhibition

7.  Internal Regulation of Enzyme Activity: Allosteric Regulation

8.  Structure of ATP

9.  Powering an Endergonic Reaction through ATP Hydrolysis: Active Transport via a Protein Pump

 

PowerPoint Presentations 

Chapter 6 Presentation (.pdf)

 

Reading Assignments and Homework

Please access the ConnectPlus site for Health Science Academy to access our reading assignments and homework.

 

Miscellaneous

1.  Here are a list of some common metabolic disorders from Medline Plus (retrieved 28 Aug 2010):

 

2.  Enzyme inhibitors are often used by pharmacia to manage the symptoms of many disorders.  Here is a summary article of drug design from Wikipedia (retrieved 28 Aug 2010).  This is a key section:

 

"Typically a drug target is a key molecule involved in a particular metabolic or signaling pathway that is specific to a disease condition or pathology, or to the infectivity or survival of a microbial pathogen. Some approaches attempt to inhibit the functioning of the pathway in the diseased state by causing a key molecule to stop functioning. Drugs may be designed that bind to the active region and inhibit this key molecule. Another approach may be to enhance the normal pathway by promoting specific molecules in the normal pathways that may have been affected in the diseased state. In addition, these drugs should also be designed in such a way as not to affect any other important "off-target" molecules or antitargets that may be similar in appearance to the target molecule, since drug interactions with off-target molecules may lead to undesirable side effects. Sequence homology is often used to identify such risks.  Most commonly, drugs are organic small molecules produced through chemical synthesis, but biopolymer-based drugs (also known as biologics) produced through biological processes are becoming increasingly more common. In addition mRNA based gene silencing technologies may have therapeutic applications."

 

An example of this application can be observed in this case study about the chemotherapeutic agent Gleevec.  This is an inhibitor of an important kinase enzyme that, when overactive, leads to a specific form of leukemia.   This exercise walks you through the process of designing drugs, in this case a cancer drug.  It really emphasizes much of what you learned this chapter. 

 

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